A variation is any change to the agreed work: more or less quantity, a changed specification, or added or deleted work. An extra item (or non-BOQ item) is work that has no item in the BOQ at all, such as an extra retaining wall the client asks for midway.
Most contracts set out how variations are instructed and priced: who can order them, how rates for new items are derived (from similar BOQ items, from market rates, or by agreement), and what happens when quantities change beyond a set limit. Those clauses differ by contract, so follow yours.
The practical rule on site: get the instruction in writing before doing the work, record measurements separately, and agree the rate early. Unapproved extras are among the most common unpaid claims. Bill extra items separately in the RA bill so they are easy to trace and approve.
Example
Illustrative: BOQ has no item for a 1.2 m compound wall extension. The client issues a written instruction; the contractor submits a rate analysis; the agreed rate is added as extra item E-1.
BOQ & budgeting in CivilPilot
BOQ, approved budgets and budget against committed and actual spend for every cost code.

